diff --git a/deploy.m b/deploy.m
index 060237e..86ed1a9 100644
--- a/deploy.m
+++ b/deploy.m
@@ -5,4 +5,17 @@
 % Ensure all folders are on the path
 addpath(genpath(path));
 
-mcc -v -m SpectralAnalysis.m -a lib/ -a src/ -a *.m
\ No newline at end of file
+% Compile preprocessing methods
+cd 'src/processing/preprocessing/'
+
+mex -largeArrayDims rebin.c
+mex -largeArrayDims synaptReplaceZeros.c
+
+cd '../../../'
+
+% Compile MEPCA methods
+cd 'src/processing/postprocessing/mepca'
+compileMEPCA
+cd '../../../../'
+
+mcc -v -m SpectralAnalysis.m -a lib/ -a src/ -a *.m -a *.mex*
\ No newline at end of file
diff --git a/lib/JSpectralAnalysis/JSpectralAnalysis.jar b/lib/JSpectralAnalysis/JSpectralAnalysis.jar
index fcd5583..2bd09a7 100644
Binary files a/lib/JSpectralAnalysis/JSpectralAnalysis.jar and b/lib/JSpectralAnalysis/JSpectralAnalysis.jar differ
diff --git a/src/gui/DataViewer.m b/src/gui/DataViewer.m
index 98c9c33..9abfb14 100644
--- a/src/gui/DataViewer.m
+++ b/src/gui/DataViewer.m
@@ -85,6 +85,7 @@
         % Buttons for interacting with the spectrum list
         addSpectrumButton;
         overlaySpectrumButton;
+        subtractSpectrumButton;
         removeSpectrumButton;
         
         switchSpectrumViewButton;
@@ -788,18 +789,59 @@ function overlaySpectrumCallback(obj)
 %                 axisHandle = axes;
                 multiSpectrumPanel = MultiSpectrumPanel(figure, obj.spectrumList.get(spectraToOverlay(1)));
                 
-                warning('No preprocessing applied...');
+                spectraToOverlayList = [];
                 
+                for i = 1:length(spectraToOverlay)
+                    if(i == 1)
+                        spectraToOverlayList = obj.spectrumList.get(spectraToOverlay(i));
+                    else
+                        spectraToOverlayList(i) = obj.spectrumList.get(spectraToOverlay(i));
+                    end
+                    
+                    if(~isempty(obj.preprocessingWorkflow))
+                        spectraToOverlayList(i) = obj.preprocessingWorkflow.performWorkflow(spectraToOverlayList(i));
+                    end
+                end
+                                
                 multiSpectrumDisplay = multiSpectrumPanel.spectrumDisplay;
                 
                 for i = 2:length(spectraToOverlay)
-                    multiSpectrumDisplay.setSpectrum(i, obj.spectrumList.get(spectraToOverlay(i)));
+                    multiSpectrumDisplay.setSpectrum(i, spectraToOverlayList(i));
                 end
                 
                 multiSpectrumDisplay.updateDisplay();
             end
         end
         
+        function subtractSpectrumCallback(this)
+            spectraToSubstract = this.spectrumListTableLastSelected(:, 1);
+            
+            if(~isempty(spectraToSubstract) && length(spectraToSubstract) == 2)
+                
+                spectrum1 = this.spectrumList.get(spectraToSubstract(1));
+                spectrum2 = this.spectrumList.get(spectraToSubstract(2));
+                
+                if(~isempty(this.preprocessingWorkflow))
+                    spectrum1 = this.preprocessingWorkflow.performWorkflow(spectrum1);
+                    spectrum2 = this.preprocessingWorkflow.performWorkflow(spectrum2);
+                end
+                
+                try 
+                    differenceSpectrum = SpectralData(spectrum1.spectralChannels, spectrum1.intensities - spectrum2.intensities);
+
+                    figure = Figure();
+                    figure.showStandardFigure();
+                    spectrumPanel = SpectrumPanel(figure, differenceSpectrum);
+                    
+                    figure.setTitle(['Difference between ' spectrum1.getDescription() ' and ' spectrum2.getDescription()]);
+                catch err 
+                    errordlg(err.message);
+                end
+            else
+                errordlg('Please select 2 spectra to subtract', 'DataViewer:NoSpectraSelected');
+            end
+        end
+        
         %% editPreprocessingWorkflow()
         function editPreprocessingWorkflow(obj)
             assignin('base', 'dataViewer', obj);
@@ -1101,6 +1143,9 @@ function createFigure(obj)
                 obj.overlaySpectrumButton = uicontrol('Parent', obj.spectrumListPanel, 'String', 'O', ...
                     'Callback', @(src, evnt) obj.overlaySpectrumCallback(), ...
                     'TooltipString', 'Overlay selected spectra');
+                obj.subtractSpectrumButton = uicontrol('Parent', obj.spectrumListPanel, 'String', 'S', ...
+                    'Callback', @(src, evnt) obj.subtractSpectrumCallback(), ...
+                    'TooltipString', 'Subtract selected spectra');
                 obj.removeSpectrumButton = uicontrol('Parent', obj.spectrumListPanel, 'String', '-', ...
                     'Callback', @(src, evnt) obj.removeSpectraFromListCallback(), ...
                     'TooltipString', 'Remove selected spectra from the list');
@@ -1291,7 +1336,8 @@ function sizeChanged(obj)
 
                         Figure.setObjectPositionInPixels(obj.addSpectrumButton, [margin, margin, panelPosition(3)/5 - margin*2, buttonHeight]);
                         Figure.setObjectPositionInPixels(obj.overlaySpectrumButton, [margin+panelPosition(3)/5, margin, panelPosition(3)/5 - margin*2, buttonHeight]);
-                        Figure.setObjectPositionInPixels(obj.removeSpectrumButton, [margin+panelPosition(3)*2/5, margin, panelPosition(3)/5 - margin*2, buttonHeight]);
+                        Figure.setObjectPositionInPixels(obj.subtractSpectrumButton, [margin+panelPosition(3)*2/5, margin, panelPosition(3)/5 - margin*2, buttonHeight]);
+                        Figure.setObjectPositionInPixels(obj.removeSpectrumButton, [margin+panelPosition(3)*3/5, margin, panelPosition(3)/5 - margin*2, buttonHeight]);
                     end
                     
                     widthForSpectrum = widthForSpectrum - widthOfSpectrumList - margin;
diff --git a/src/gui/RegionOfInterestListEditor.m b/src/gui/RegionOfInterestListEditor.m
index 0f6a8c5..741b56c 100644
--- a/src/gui/RegionOfInterestListEditor.m
+++ b/src/gui/RegionOfInterestListEditor.m
@@ -12,6 +12,8 @@
         editROIButton;
         removeROIButton;
         
+        autoROIButton;
+        
         regionOfInterestEditor = 0;
         
         roiFinishedEditingListener = 0;
@@ -70,6 +72,22 @@ function addRegionOfInterestCallback(this)
                 'FinishedEditing', @(src, evnt)this.finishedEditingRegionOfInterest(src.getRegionOfInterest()));
         end
         
+        function autoRegionOfInterestCallback(this)
+            for i = 1:this.image.getHeight()
+                newROI = RegionOfInterest(this.image.getWidth(), this.image.getHeight());
+                newROI.setName(['Line ' num2str(i)]);
+                
+                roi = zeros(this.image.getHeight(), this.image.getWidth());
+                roi(i, :) = 1;
+                
+                newROI.addPixels(roi);
+                
+                this.regionOfInterestList.add(newROI);
+                
+                this.updateRegionOfInterestList();
+            end
+        end
+        
         function finishedEditingRegionOfInterest(this, regionOfInterest)
             if(~isa(regionOfInterest, 'RegionOfInterest'))
                 exception = MException('RegionOfInterestListEditor:InvalidArgument', 'addRegionOfInterest: Must suply a RegionOfInterest.');
@@ -197,6 +215,9 @@ function createFigure(this)
                 'Units', 'normalized', 'Position', [0.6 0.125 0.1 0.05], 'Callback', @(src, evnt) this.editRegionOfInterest());
             this.removeROIButton = uicontrol(this.handle, 'String', '-', ...
                 'Units', 'normalized', 'Position', [0.6 0.05 0.1 0.05], 'Callback', @(src, evnt) this.removeRegionOfInterestCallback());
+            
+            this.autoROIButton = uicontrol(this.handle, 'String', 'Auto Line', ...
+                'Units', 'normalized', 'Position', [0.8 0.2 0.1 0.05], 'Callback', @(src, evnt) this.autoRegionOfInterestCallback());
         end
     end
 end
\ No newline at end of file
diff --git a/src/processing/postprocessing/mepca/compile.m b/src/processing/postprocessing/mepca/compileMEPCA.m
similarity index 93%
rename from src/processing/postprocessing/mepca/compile.m
rename to src/processing/postprocessing/mepca/compileMEPCA.m
index a9181b0..27b168a 100644
--- a/src/processing/postprocessing/mepca/compile.m
+++ b/src/processing/postprocessing/mepca/compileMEPCA.m
@@ -1,4 +1,3 @@
-mex -largeArrayDims rebin.c
 mex -largeArrayDims calculateE.c
 mex -largeArrayDims updateQ.c
 
diff --git a/src/processing/preprocessing/InterpolationRebinZeroFilling.m b/src/processing/preprocessing/InterpolationRebinZeroFilling.m
index 7664fb5..0b2e01b 100644
--- a/src/processing/preprocessing/InterpolationRebinZeroFilling.m
+++ b/src/processing/preprocessing/InterpolationRebinZeroFilling.m
@@ -19,6 +19,7 @@
             sChannels = obj.Parameters(1).value:obj.Parameters(3).value:obj.Parameters(2).value;
 
             intensities = interp1(spectralChannels, intensities, sChannels);
+            intensities(isnan(intensities)) = 0;
             spectralChannels = sChannels;
         end
     end